I have a series of T1w volumes with gadolinium signal present…and I’m having difficulty registering them to an atlas volume (AFNI_18.0.26, auto_warp.py, MNI_T1_2009c+tlrc). Specifically, 3dQwarp seems to interpret the vessels as ‘brain,’ and wraps them around cortical folds. Is there any principled way to remove the gadolinum signal, while sparing brain?
I haven’t seen this myself, but I am perfectly willing to guess how to solve this.
- Use 3dQwarp’s exclusion mask -emask. You will need to create a mask image from just those voxels, maybe by thresholding and/or clustering.
- Smooth the vessels away with gaussian blurs.
- Hide the vessels by zeroing them out or reducing the intensities. For both this method and the previous one, you can still apply the warp to the original data.